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Yorodumi- PDB-4zc1: Crystal Structure of type II Dehydroquinate dehydratase from Acin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zc1 | ||||||
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Title | Crystal Structure of type II Dehydroquinate dehydratase from Acinetobacter baumannii with a different crystal form at 2.52 A Resolution | ||||||
Components | 3-dehydroquinate dehydratase | ||||||
Keywords | LYASE / 3-DEHYDROQUINASE / TYPE II DHQASE | ||||||
Function / homology | Function and homology information 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Iqbal, N. / Kumar, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of type II Dehydroquinate dehydratase from Acinetobacter baumannii with different crystal form at 2.52 A Resolution Authors: Iqbal, N. / Kumar, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zc1.cif.gz | 340.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zc1.ent.gz | 280 KB | Display | PDB format |
PDBx/mmJSON format | 4zc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/4zc1 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/4zc1 | HTTPS FTP |
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-Related structure data
Related structure data | 4rc9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16007.288 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 17978 / NCDC KC 755) (bacteria) Strain: ATCC 17978 / NCDC KC 755 / Gene: aroQ, A1S_2009 / Plasmid: Pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: A3M692, 3-dehydroquinate dehydratase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.95 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG3350, MgSO4, Tris buffer / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 77 K / Ambient temp details: CCD |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 14, 2014 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→50 Å / Num. all: 248902 / Num. obs: 62069 / % possible obs: 100 % / Redundancy: 4 % / Rsym value: 0.1 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.52→2.56 Å / Redundancy: 4 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RC9 Resolution: 2.52→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.859 / SU B: 13.157 / SU ML: 0.286 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.15 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.165 Å2
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Refinement step | Cycle: 1 / Resolution: 2.52→50 Å
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Refine LS restraints |
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